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- PDB-7up2: NDM1-inhibitor co-structure -

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Basic information

Entry
Database: PDB / ID: 7up2
TitleNDM1-inhibitor co-structure
ComponentsBeta-lactamase VIM-1
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Metallo-beta-lactamase inhibitor / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase / hydrolase activity / metal ion binding
Similarity search - Function
: / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like
Similarity search - Domain/homology
Chem-NZR / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.13 Å
AuthorsScapin, G. / Fischmann, T.O.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Med.Chem. / Year: 2022
Title: Rapid Evolution of a Fragment-like Molecule to Pan-Metallo-Beta-Lactamase Inhibitors: Initial Leads toward Clinical Candidates.
Authors: Mandal, M. / Xiao, L. / Pan, W. / Scapin, G. / Li, G. / Tang, H. / Yang, S.W. / Pan, J. / Root, Y. / de Jesus, R.K. / Yang, C. / Prosise, W. / Dayananth, P. / Mirza, A. / Therien, A.G. / ...Authors: Mandal, M. / Xiao, L. / Pan, W. / Scapin, G. / Li, G. / Tang, H. / Yang, S.W. / Pan, J. / Root, Y. / de Jesus, R.K. / Yang, C. / Prosise, W. / Dayananth, P. / Mirza, A. / Therien, A.G. / Young, K. / Flattery, A. / Garlisi, C. / Zhang, R. / Chu, D. / Sheth, P. / Chu, I. / Wu, J. / Markgraf, C. / Kim, H.Y. / Painter, R. / Mayhood, T.W. / DiNunzio, E. / Wyss, D.F. / Buevich, A.V. / Fischmann, T. / Pasternak, A. / Dong, S. / Hicks, J.D. / Villafania, A. / Liang, L. / Murgolo, N. / Black, T. / Hagmann, W.K. / Tata, J. / Parmee, E.R. / Weber, A.E. / Su, J. / Tang, H.
History
DepositionApr 14, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 8, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-lactamase VIM-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4564
Polymers26,0101
Non-polymers4463
Water4,774265
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.560, 67.420, 40.180
Angle α, β, γ (deg.)90.000, 91.670, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Beta-lactamase VIM-1 / Class B carbapenemase VIM-1 / Metallo-beta-lactamase / Metallo-beta-lactamase VIM-1 / Metallobeta- ...Class B carbapenemase VIM-1 / Metallo-beta-lactamase / Metallo-beta-lactamase VIM-1 / Metallobeta-lactamase / Subclass B1 metallo-beta-lactamase VIM-1 / VIM-1 / VIM-1 metallo-beta-lactamase / VIM-1 protein


Mass: 26009.799 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: blaVIM, blaVIM-1, CAZ10_38240, CAZ10_38245 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9XAY4
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-NZR / (2M)-4'-methyl-2-(2H-tetrazol-5-yl)[1,1'-biphenyl]-3-sulfonamide


Mass: 315.350 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H13N5O2S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 265 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.06 Å3/Da / Density % sol: 40.27 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: .2 M magnesium chloride 0.1 M tris hydrochloride pH 8.5 25.0 w/v polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 7, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.13→67.42 Å / Num. obs: 75372 / % possible obs: 96.6 % / Redundancy: 3.3 % / Biso Wilson estimate: 11.84 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.036 / Rrim(I) all: 0.065 / Net I/σ(I): 11.9 / Num. measured all: 247297
Reflection shell

Diffraction-ID: 1 / Redundancy: 3.3 %

Resolution (Å)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.13-1.180.5312768083660.7590.3410.6322.195.1
4.08-67.420.038568816980.9950.0250.04630.598.1

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.1.27data scaling
BUSTER2.11.4refinement
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ZR9

3zr9


Resolution: 1.13→16.54 Å / Cor.coef. Fo:Fc: 0.9695 / Cor.coef. Fo:Fc free: 0.9652 / SU R Cruickshank DPI: 0.032 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.033 / SU Rfree Blow DPI: 0.033 / SU Rfree Cruickshank DPI: 0.033
RfactorNum. reflection% reflectionSelection details
Rfree0.1731 3788 5.03 %RANDOM
Rwork0.1618 ---
obs0.1624 75306 95.69 %-
Displacement parametersBiso max: 101.54 Å2 / Biso mean: 19.48 Å2 / Biso min: 7.79 Å2
Baniso -1Baniso -2Baniso -3
1--2.1276 Å20 Å20.4699 Å2
2--1.8746 Å20 Å2
3---0.253 Å2
Refine analyzeLuzzati coordinate error obs: 0.137 Å
Refinement stepCycle: final / Resolution: 1.13→16.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1719 0 24 266 2009
Biso mean--16.92 31.97 -
Num. residues----230
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d596SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes46HARMONIC2
X-RAY DIFFRACTIONt_gen_planes281HARMONIC5
X-RAY DIFFRACTIONt_it1822HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion239SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2333SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1822HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg2510HARMONIC21.12
X-RAY DIFFRACTIONt_omega_torsion4.9
X-RAY DIFFRACTIONt_other_torsion15.34
LS refinement shellResolution: 1.13→1.16 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2119 246 4.87 %
Rwork0.2031 4804 -
all0.2036 5050 -
obs--95.69 %
Refinement TLS params.Method: refined / Origin x: -16.8396 Å / Origin y: -2.5831 Å / Origin z: -5.2855 Å
111213212223313233
T-0.0573 Å2-0.0085 Å2-0.005 Å2--0.0415 Å2-0.0034 Å2---0.0239 Å2
L0.9666 °2-0.3414 °2-0.372 °2-1.1051 °20.3056 °2--1.1029 °2
S-0.0155 Å °-0.0043 Å °0.0438 Å °-0.0449 Å °0.015 Å °-0.0459 Å °-0.0004 Å °0.004 Å °0.0005 Å °
Refinement TLS groupSelection details: { A|* }

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